The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Abstract

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism

“…The statistical tests of analysis of variance and t test were done using the R core package (R Development Core Team, 2011), and the BH method (Benjamini and Hochberg, 1995) was used for multiple testing correction of the t test P values. All of the bioinformatics and statistical analyses were done either on our local servers or on the iPLANT Atmosphere cloud server (Goff et al, 2011).…”

Empirical Analysis of HPC Using Different Programming Models

“…Furthermore, results in figure 9 are giving positive aspect to consider parallel programming models as hybrid in order to achieve HPC. The operation used in our experiments might be smaller as compared to other massive level computation requiring problems such as Computational Fluid Dynamics (CFD) [24], Cholesky decomposition [25], LU complexity operation [26] etc and many more in different fields. …”

Teaching Data Science and Cloud Computing in Low and Middle Income Countries

“…For comparison, a similar short-course was presented at the Nottingham UK, Sutton Bonington Campus (UoN-SB: 2010-2014) and equivalent transcriptomics practicals were delivered at Huazhong Agricultural University, Wuhan, China (HAU: 2014). Student numbers in Nottingham and Wuhan were high (50+) and in Namibia and Malaysia were half the size of the CCC courses [15][16][17][18][19][20]. Many of the experiences were analogous to those experienced in CCC but a few differences may be instructive.…”

“…The third short-course transcriptomics practical added in 2014 was a remote analysis of RNAseq data in DNAsubway at iPlant (http://dnasubway.iplantcollaborative.org) [17]. This required the students to (optionally) register with a valid email address during the practical in order to access the RNAseq file store.…”